Breakthrough reported in creating artificial genetic code

Scientists reported Wednesday that they had taken a significant step toward altering the fundamental alphabet of life — creating for the first time an organism with artificial building blocks in its genetic code.

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By ANDREW POLLACKNew York Times News Service

capecodtimes.com

By ANDREW POLLACKNew York Times News Service

Posted May. 7, 2014 at 5:05 PM
Updated May 7, 2014 at 5:23 PM

By ANDREW POLLACKNew York Times News Service

Posted May. 7, 2014 at 5:05 PM
Updated May 7, 2014 at 5:23 PM

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Scientists reported Wednesday that they had taken a significant step toward altering the fundamental alphabet of life — creating for the first time an organism with artificial building blocks in its genetic code.

The accomplishment might eventually lead to organisms that can make medicines or industrial products that cannot be made by cells with only natural DNA. The scientists behind the work at the Scripps Research Institute have already formed a company to try to use the technique to develop new antibiotics, vaccines and other products.

The work also gives some backing to the concept that life can exist elsewhere in the universe using genetics different from that on Earth.

“This is the first time that you have had a living cell manage an alien genetic alphabet,” said Steven A. Benner, a researcher in the field at the Foundation for Applied Molecular Evolution in Gainesville, Fla., who was not involved in the new work.

But the research, published online by the journal Nature, is bound to raise safety concerns and questions about whether man is playing God. The new paper could intensify calls for greater regulation of the budding field known as synthetic biology, which involves the creation of biological systems designed for specific purposes.

“The arrival of this unprecedented ‘alien’ life form could in time have far-reaching ethical, legal and regulatory implications,” Jim Thomas of the ETC Group, a Canadian advocacy organization, said in an email. “While synthetic biologists invent new ways to monkey with the fundamentals of life, governments haven’t even been able to cobble together the basics of oversight, assessment or regulation for this surging field.”

Despite the great diversity of life on Earth, all species, from simple bacteria to man, use the same genetic code. It consists of four chemical units in DNA, sometimes called nucleotides or bases, that are usually represented by the letters A, C, G and T. The sequence of these chemical units determines what proteins the cell makes.

What the Scripps researchers did was to chemically synthesize two new nucleotides, which they called X and Y. They inserted an X-Y pair into the common bacterium E. coli. The bacteria were able to reproduce normally, replicating the X and Y along with the natural nucleotides.

In effect, the bacteria have a genetic code of six letters rather than four, perhaps allowing them to make novel proteins.

“If you have a language that has a certain number of letters, you want to add letters so you can write more words and tell more stories,” said Floyd E. Romesberg, a chemist at Scripps who led the work.

Romesberg said the technique was safe because the synthetic nucleotides are fed to the bacteria. Should the bacteria escape into the environment or enter someone’s body, they would not be able to obtain the needed material and would either die or revert to using only natural DNA. “This could never infect something,” he said.

That is one reason his new company, Synthorx, is looking at using the technique to grow viruses or bacteria to be used as live vaccines. Once in the bloodstream, they would conceivably induce an immune response but not be able to reproduce.

One possible use of an expanded genetic alphabet is to allow cells to make new types of proteins.

Combinations of three nucleotides in DNA, also sometimes called bases, specify particular amino acids. The sequence TCT, for instance, specifies the amino acid serine, while AGG specifies arginine. The cell, following these instructions, strings amino acids together to form proteins. With rare exceptions, living things use only 20 amino acids.

But there are hundreds of other amino acids that could conceivably be used in proteins, potentially adding new functions. Ambrx, a San Diego company that has filed to go public, is incorporating novel amino acids into certain proteins that are used as drugs in an effort to make the drugs more potent in killing tumors or longer-lasting in the bloodstream.

But it is difficult now to engineer cells genetically to handle more than one novel amino acid. That is because almost all the possible three-letter DNA combinations are already used to specify one of the existing 20 amino acids. There are no words left that can be used to tell the cell to use a novel amino acid.

But if there were six DNA letters, there would be many possible new three-letter combinations.

Work on artificial nucleotides has been underway for more than 20 years. They have functioned in test tubes and are even used in some diagnostic tests.

But until now it has not been possible to get them to function in a living cell. Romesberg said he and his colleagues created 300 variants before coming up with nucleotides that would be stable enough and would be replicated as easily as the natural ones when the cells divide. The X nucleotide pairs with Y, just as A pairs with T and C pairs with G, allowing the DNA to be accurately replicated.

The bacteria described in the Nature paper each contained only a single X-Y pair. It is not yet known whether a cell would function if it contained many such pairs. It is also not clear how long the bacteria will survive. The paper mentions growing them for only 24 replications over about 15 hours.

Most important, the researchers have not yet demonstrated that the artificial nucleotides can be transcribed into RNA and then used to make proteins. That will require more genetic engineering of the bacteria, though work by others has suggested how it might be done.

The Scripps researchers first engineered a circular piece of DNA called a plasmid containing the novel nucleotides and put it into the bacteria. But in order to replicate, the bacteria would need to make more of the foreign nucleotides.

Benner in Florida is trying to engineer cells genetically so they can make their own nonnatural nucleotides. That would allow the cells to survive on their own.

But Romesberg and colleagues took a shortcut of sorts. Chloroplasts in plants have the ability to import nucleotides from the surrounding tissue, and other researchers have figured out the genes responsible for this. The Scripps researchers spliced an algae gene into E. coli, giving the bacteria the ability to take up the X and Y nucleotides from the medium in which they grew.

“It took some clever problem-solving to get where they got,” said Eric T. Kool, a professor of chemistry at Stanford University who is also doing research in the area. “It is clear that the day is coming that we’ll have stably replicating unnatural genetic structures.”

Besides any possible practical applications, the research into the field, which is sometimes called xenobiology, could shed light on why living things evolved to have four nucleotides and whether there could be true alien life with other arrangements. It could be that four is the most efficient number, in which case organisms with expanded genetic codes might not function very well.